Jekyll2023-12-01T17:34:06+00:00/feed.xmlFraternali LabFraternali Lab @ ISMB, UCLFraternali LabsciCSR method published in Nature Methods2023-11-06T00:00:00+00:002023-11-06T00:00:00+00:00/sciCSR-paper<p><img src="/assets/images/sciCSR-paper-website.jpg" alt="image-center" class="align-center" /></p>
<p>Joseph’s paper on the new computational method, sciCSR, for analysing class-switch recombination (CSR) in B cells single-cell RNA sequencing data, has been published in Nature Methods!</p>
<p>Read the paper on <a href="https://www.nature.com/articles/s41592-023-02060-1">Nature Methods</a>. We have also written a behind-the-paper Research Briefing article which can be found <a href="https://www.nature.com/articles/s41592-023-02061-0">here</a>.</p>Fraternali LabStudies of B cells in melanoma published in Nature Communications2023-06-09T00:00:00+01:002023-06-09T00:00:00+01:00/Melanoma-B-cells<p><img src="/assets/images/skin-cancer-cells.png" alt="image-center" class="align-center" /></p>
<p>Our collaboration to study B-cells in melanoma, with the group of Sophia Karagiannis at King’s, has just been published in Nature Communications! Here, we collaborated with the Karagiannis to analyse antibody repertoire from B cells infiltrated in melanoma tissues. We described features in these repertoires and drew parallel with autoimmunity.</p>
<p>Read the paper on <a href="https://doi.org/10.1038/s41467-023-39042-y">Nature Communications</a>. We also have a news story on this work, on the <a href="https://www.kcl.ac.uk/news/study-uncovers-how-b-cells-react-to-skin-cancer">King’s web page</a>.</p>Fraternali LabNanocapsule work received NPL Rayleigh Award2021-10-18T00:00:00+01:002021-10-18T00:00:00+01:00/rayleigh-award<p><img src="/assets/images/peptide-nanoparticles.png" alt="image-center" class="align-center" /></p>
<p>Irene’s paper on simulating an antimicrobial nanocapsule on lipid membranes has been awarded the Rayleigh award from the National Physical Laboratory!</p>
<p>Read the story on <a href="https://www.kcl.ac.uk/news/kings-academics-receive-national-physics-laboratorys-most-prestigious-award">King’s website</a>. The paper was published on <a href="https://pubs.acs.org/doi/10.1021/acsnano.9b06814">ACS Nano</a>.</p>Fraternali LabAntimcrobial nanocapsule design and dynamics published in the Nanoscale journal2021-06-17T00:00:00+01:002021-06-17T00:00:00+01:00/irene-nanoscale<p><img src="/assets/images/slider/Irene_Nanoscale_capsule.png" alt="image-center" class="align-center" /></p>
<p>Irene and Carlos’ work on designing and simulating the molecular dynamics of antimicrobial capsules has been published in the journal <a href="https://doi.org/10.1039/D0NR08146A"><em>Nanoscale</em></a>! Great milestone for all the time and effort put into this project!</p>Fraternali LabZoomVar variant database published in PLoS Biology2021-05-30T00:00:00+01:002021-05-30T00:00:00+01:00/zoomvar-published<p><img src="/assets/images/slider/zoomvar.png" alt="image-center" class="align-center" /></p>
<p>We are delighted that the <a href="http://fraternalilab.kcl.ac.uk/ZoomVar">ZoomVar</a> database is published in the journal <a href="https://doi.org/10.1371/journal.pbio.3001207">PLoS Biology</a>! Hopefully this tool will be of use to many in annotating protein-level information for missense variants! Congratulation to Anna who began the project and Joseph who pushed this to publication!</p>Fraternali LabscRNAseq analysis of peripheral B cell populations2020-11-01T00:00:00+00:002020-11-01T00:00:00+00:00/pure-published<p><img src="/assets/images/pure1.jpg" alt="image-center" class="align-center" /></p>
<p>Our collaboration with the Dunn-Walters group at University of Surrey has reached a new milestone with our new work on <a href="https://doi.org/10.3389/fimmu.2021.602539">Frontiers in Immunology</a>! This is our first venture into single-cell RNA sequencing to describe transcriptomic features of different B cell populations. We applied RNA velocity estimation and analysed the transitions between these different cell subpopulations!</p>Fraternali LabPapers on screening protein-protein interaction inhibitor using crystal lattices2020-08-01T00:00:00+01:002020-08-01T00:00:00+01:00/interfacescreen<p><img src="/assets/images/interface_crystal_screen.png" alt="image-center" class="align-center" /></p>
<p>We celebrate two papers on a new <em>in silico</em> method to screen existing crystal lattices available in the Protein Data Bank, for lattices suitable for carrying out fragment soaking experiments to design chemical inhibitors targeting protein-protein interactions! See this paper in <a href="https://doi.org/10.1021/acs.jmedchem.0c00403">J Med Chem</a> for description and application on two attractive therapeutic targets (p38-alpha and interleukin-1-beta).</p>
<p>In a subsequent work now published in <a href="https://doi.org/10.3389/fphar.2020.615211">Frontiers in Pharmacology</a> we apply the method to analyse existing lattices containing the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. Our collaborator Gian-Felice de Nicola at the Randall has managed to generate a novel crystal form which exposes the interface between RBD and ACE2, making it available for fragment screening to develop inhibitors that target this interaction!</p>Fraternali LabIrene’s work has been featured on The Times!2020-02-25T00:00:00+00:002020-02-25T00:00:00+00:00/irene-times<p><img src="/assets/images/capsule.jpeg" alt="image-center" class="align-center" /></p>
<p>We are very happy that Irene’s work on simulating self-assembly of an antimicrobial nanocapsule has been featured on <a href="https://www.thetimes.co.uk/article/man-made-antibacterial-virus-offers-hope-in-superbug-fight-0pv25ld2t">The Times</a>.</p>
<p>Read the story on <a href="https://www.kcl.ac.uk/news/kings-scientists-help-develop-artificial-virus-to-combat-superbugs">King’s website</a>. The paper was published on <a href="https://pubs.acs.org/doi/10.1021/acsnano.9b06814">ACS Nano</a>.</p>Fraternali LabSymposium on Networks and Machine Learning @ The Crick2020-01-04T00:00:00+00:002020-01-04T00:00:00+00:00/crick-network-symposium<p><img src="/assets/images/network_test.png" alt="image-center" class="align-center" /></p>
<p>The Systems and Network Medicine Forum is hosting a <strong>Symposium on Network Analysis and Machine Learning Applications in Biology</strong>, on <strong>Monday 3rd February, 09:00am-13:00pm</strong> in <strong>The Francis Crick Institute</strong> (1 Midland Road, London).</p>
<p>Invited talks:
Prof Santo Fortunato, Director of the IU Networks Science Institute (IUNI), USA
Dr. Andela Šarić, Associate Professor, Institute for the Physics of Living Systems, UCL, UK
Dr Alessia Annibale, Senior Lecturer in Disordered Systems, King’s College London, UK
Dr. Andreas Bender, Reader for Molecular Informatics, University of Cambridge, UK
Prof Mauricio Barahona, Chair in Biomathematics, Imperial College London, UK
Dr. Rob Ewing, Associate Professor in Proteomics and Systems Biology, University of Southampton, UK</p>
<p>The event will be concluded by a student presentations and a networking session.</p>
<p>Please find the full agenda and registration details via <a href="https://www.eventbrite.co.uk/e/symposium-on-networks-and-machine-learning-in-biology-tickets-86917258861?utm-medium=discovery&utm-campaign=social&utm-content=attendeeshare&aff=escb&utm-source=cp&utm-term=listing">Eventbrite</a>.</p>
<p>PhD students and Postdoctoral researchers that would like to present their work on Machine Learning, AI and Network Analytics methods and biomedical applications in the Early Researcher Presentation Session, please send a 100 word summary to <a href="mailto:konstantinos.theofilatos@kcl.ac.uk">konstantinos.theofilatos@kcl.ac.uk</a> by <strong>17th January, 12pm</strong>.</p>
<p>This event is organised by Systems and Network Medicine Forum. Systems and Network Medicine Forum is a collaborative network funded by the Crick Networking Fund with members from KCL (Dr. Konstantinos Theofilatos, Prof. Manuel Mayr, Prof. Franca Fraternali, Dr. Sophia Tsoka), UCL (Prof. Lazaros Papageorgiou), Imperial College (Prof. Michael Sternberg, Prof. Marc-Emmanuel Dumas) and The Francis Crick Institute (Prof. Jernej Ule, Prof. Markus Ralser, Dr. Aengus Stewart).</p>Fraternali LabNew paper on eLife2019-07-25T00:00:00+01:002019-07-25T00:00:00+01:00/jamie-elife<p><img src="/assets/images/jamie_elife_assembled.png" alt="image-center" class="align-center" /></p>
<p>Our lab has just published a <a href="https://elifesciences.org/articles/45068">new paper on eLife</a>, investigating the allosteric effects of multiple ligands on the PKM2 enzyme – superb experimental and computational investigations + plus a new package AlloHubMat – a PhD-worth piece of work! Congratulations to Jamie!</p>Fraternali Lab